A spin-1 representation for dual-funnel energy landscapes

Elenewski, Justin E.; Velizhanin, Kirill A.; Zwolak, Michael

doi:10.1063/1.5036677

Title: A spin-1 representation for dual-funnel energy landscapes

Journal Article · Fri Jul 20 00:00:00 EDT 2018 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.5036677· OSTI ID:1471315

Elenewski, Justin E. ^[1];

^[2];

^[3]

National Inst. of Standards and Technology (NIST), Gaithersburg, MD (United States); Univ. of Maryland, College Park, MD (United States)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
National Inst. of Standards and Technology (NIST), Gaithersburg, MD (United States)

The interconversion between the left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape. In this context, the funnel minima are connected through a continuum of unfolded conformations, evocative of the classical helix-coil transition. Physical intuition and recent conjectures suggest that this landscape can be mapped by assigning a left- or right-handed helical state to each residue. In this study, we explore this possibility using all-atom replica exchange molecular dynamics and an Ising-like model, demonstrating that the energy landscape architecture is at odds with a two-state picture. A three-state model—left, right, and unstructured—can account for most key intermediates during chiral interconversion. Additionally, competing folds and excited conformational states still impose limitations on the scope of this approach. However, the improvement is stark: Moving from a two-state to a three-state model decreases the fit error from 1.6 k_BT to 0.3 k_BT along the left-to-right interconversion pathway.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); USDOE Laboratory Directed Research and Development (LDRD) Program

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1471315

Report Number(s):: LA-UR-18-28756

Journal Information:: Journal of Chemical Physics, Vol. 149, Issue 3; ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 2 works

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Topology, Landscapes, and Biomolecular Energy Transport Elenewski, Justin E.; Velizhanin, Kirill A.; Zwolak, Michael arXiv https://doi.org/10.48550/arxiv.1904.11154	text	January 2019
Topology, landscapes, and biomolecular energy transport Elenewski, Justin E.; Velizhanin, Kirill A.; Zwolak, Michael Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12700-w	journal	October 2019

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